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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely,
AFNI HQ
History of AFNI updates
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Pages: 123
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Thanks Rick!
That totally make sense. Just in case other people with similar preference of analyzing in orig space make the same mistake of start modifying command from this recommended example, I suggest adding just a bit of warning in the doc page against my usage or throw out some error message if people use the same combination of options I used. Maybe some explanation about this was already
by
Mingbo
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AFNI Message Board
Thanks!
The reason of wanting the data to be in orig space is to minimize warping and resampling done to the epi data. And I think the script might have also got some failure when I tried to warp to standard space. But having an alignment with the template will allow warping of atlases into the orig space.
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Mingbo
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AFNI Message Board
Hi,
I was recently trying to adapt Example 11 of the documentation of afni_proc.py for my project.
The command is as below:
afni_proc.py -out_dir $subj.results -subj_id $subj -blocks despike tshift align tlrc volreg mask scale regress \
-script $subj/proc.$subj.test -scr_overwrite \
-radial_correlate_blocks volreg \
-copy_anat $fs_dir/brain.finalsurfs.nii.gz \
by
Mingbo
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AFNI Message Board
Postdoctoral Researcher position on fMRI study of spontaneous thoughts and natural task
We seek a talented neuroscientist with extensive experience in the areas of advanced fMRI analysis, (such as encoding or decoding models) and the design of experiments using naturalistic tasks and assessing spontaneous thoughts. A 3-year postdoctoral position is available at Dr. Mingbo Cai’s lab at the Intern
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Mingbo
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AFNI Message Board
Hello,
I noticed that the output resolution of the EPI file by afni_proc.py does not reflect what the documentation says.
The documentation says this for the parameter -volereg_warp_dxyz.
-volreg_warp_dxyz DXYZ : grid dimensions for _align_e2a or _tlrc_warp
e.g. -volreg_warp_dxyz 3.5
default: min dim truncated to 3 significant bits
And it listed a
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Mingbo
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AFNI Message Board
It was my fault. I put wrong output directory for the motion parameter files.
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Mingbo
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AFNI Message Board
Hello,
I just saw this message today when running 3dvolreg on ubuntu 16.06. I updated my AFNI and it still exists. I found the same problem with an old version and the most updated version of AFNI on a cluster which runs redhat 7.
Fatal Signal 11 (SIGSEGV) received
3dvolreg main
Bottom of Debug Stack
** Command line was:
3dvolreg -prefix NULL -1Dmatrix_save ../preprocessed/sub-
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Mingbo
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AFNI Message Board
Hi Daniel,
Thank you!
It seems to me that $FREESURFER_HOME points to the right location:
$ ls $FREESURFER_HOME
ASegStatsLUT.txt FreeSurferEnv.sh sessions
AUTHORS fsafd SetUpFreeSurfer.csh
average fsfast SetUpFreeSurfer.sh
bin lib Simple_surface_labels2009.txt
build-stamp.txt LICEN
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Mingbo
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AFNI Message Board
Hi,
I tried @FS_roi_label -name ALL -labeltable aparc+aseg_rank.lt -rankmap aparc+aseg_rank.rankmap.1D command and got the exact same error. But surprisingly this only happens to one of the cluster we are using here but not the other.
Do you know what might be the cause of this?
Thanks!
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Mingbo
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AFNI Message Board
Hi,
Actually I found these messages in the log of @SUMA_Make_Spec_FS:
Program 3dmerge
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (64.0 MB)
.-- Wrote edited dataset: ./aparc+aseg_rank.nii
sed: -e expression #1, char 4: unknown command: `0'
li: Subscript out of range.
Failed to make roi labels for mri/aparc+aseg.mgz
Any idea why this h
by
Mingbo
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AFNI Message Board
Hi,
I find it a bit strange that in the SUMA folder of some subjects that I recently run, the *niml.lt files are missing. I thought they are automatically generated by @SUMA_Make_Spec_FS, yes? I checked the log of recon-all and @SUMA_Make_Spec_FS but there are no errors. Can you tell me how I can find the index of each brain region from SUMA folder?
Thanks!
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Mingbo
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AFNI Message Board
Hi,
It seems that if I keep saving files in nifti format (for example by 3dZeropad), the tilt angle of an oblique dataset is lost. (3dinfo says its orientation is plumb). I wonder if there is any way to add back the tilt angle? The loss of tilt angle seems to make the job more difficult for align_epi_anat.py.
Thanks!
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Mingbo
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AFNI Message Board
Ah, I see. I typically think that Z should be I-S direction. But this program really just takes the last dimension in data as Z.
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Mingbo
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AFNI Message Board
Hi Rick,
Thanks! Here is the command I used:
3dZcutup -keep 29 101 -prefix topup2.5GRAPPA_iout_alzc.nii topup2.5GRAPPA_iout_al+orig.
++ 3dZcutup: AFNI version=AFNI_16.1.25 (Jun 15 2016) [64-bit]
*** -keep 29 101 goes past last slice 69
The 3dinfo output of the dataset is below:
3dinfo topup2.5GRAPPA_iout_al+orig.
++ 3dinfo: AFNI version=AFNI_16.1.25 (Jun 15 2016) [64-bit]
Dataset
by
Mingbo
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AFNI Message Board
Hi,
I am trying to use 3dZcutup to cut slices of a dataset which happens to be saved in ASR orientation. As I supply the range of slices to keep to the command, it tells me that my slice indices pass the number of slices while it does not. Apparently the slice count i this case is in R-L direction. So I suppose 3dZcutup just assumes data is saved such that the last dimension is z dimension.
Can
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Mingbo
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AFNI Message Board
Hi Gang,
Thanks! That is probably the last resort to go. But if by any chance you can make stim_times_IM compatible to other HRF bases than dmBLOCK, it would be great!
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Mingbo
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AFNI Message Board
Hi,
I am wondering if it is possible to use other HRF than dmBLOCK with -stim_times_IM option of 3dDeconvolve?
Right now when I try SPMG1, it gives me an error saying that my timing files has one modulation parameter which is not legal. But in fact my timing file only has a stim onset parameter and a duration parameter (for example: 10.0:3.0). The same timing file works if I use dmBLOCK.
Tha
by
Mingbo
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AFNI Message Board
Hi,
I am using the slow_surf_clustsim.py to estimate the cluster size for multiple comparison.
One thing I found strange was that on one hemisphere of a subject, during a step that the script seem to be doing iterative smoothing until the targeted FWHM level, the FWHM actually decreases after it reaches a peak. I have not fully understood this iterative process. But I assume it is applying t
by
Mingbo
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AFNI Message Board
Hi,
I have a problem using 3dMEMA on surface data.
I have done all the analysis on standard mesh with ld=60. On individual subject, 3dDevonvolve was done to get coef and Tstat for each regressor and the -bucket option was used to save the data. When viewing on individual subject in suma, the result looks very reasonable. I set the AFNI_NIML_TEXT_DATA environment parameter to YES just so that I
by
Mingbo
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AFNI Message Board
Hi Ziad,
Thanks for pointing out the village of the same name! I do not know that village before but I am glad we have the same name. It looks like you are going to do some mountain climbing?
Further on the original topic: if I understand correctly, in your reply, x,y,z are coordinate in source coordinate and x',y',z' are in base coordinates. If so, and if the base is anatomy
by
Mingbo
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AFNI Message Board
Hello,
When I used the -EPI option of 3dAllineate, my understanding was that it restricts the scaling and shearing only in y-direction. For scaling it is easy to understand, but for shearing, what exactly is this restriction? I asked because I saw an output of final fit parameter like the following:
+ Final fine fit Parameters:
x-shift=-0.6944 y-shift= 0.0726 z-shift= 0.1699
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Mingbo
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AFNI Message Board
Thanks Rick,
I believe that should work. But because our dicom images are not named that perfect, it will probably take the same effort as to extract time offset from the last image to a file and use the @filename option in to3d for automating everything. Anyway I suggest adding an option to specify which dicom to use (second, last, etc.) in to3d if you have spare time in future. This should als
by
Mingbo
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AFNI Message Board
Hello,
I have noticed some problem of getting correct slice timing of multiband fMRI data generated by the custom sequence built by CMRR of University of Minnesota. For reference of their slice timing, here is a link. We use Siemens Trio scanner with 32 channel coil.
The command I used for to3d was like this:
to3d -epan -prefix empty_run.01 -assume_dicom_mosaic -oblique_origin -time:zt 58
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Mingbo
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AFNI Message Board
Oh, I think I solved it.
I have linked the file at another directory. It succeeded after I deleted the link.
by
Mingbo
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AFNI Message Board
Hi Gang,
I thought I sent a PM to you but did not see it in the sent box. I was not sure if it was sent so I posted here.
I warped an ROI mask with 3dAllineate. I found that I could not load the file after warping, but could load the source file.
Here is the error I got:
>> = BrikLoad ('mask.DvCpos.pthre.aligned.event_run.01+orig')
Unzipping mask.DvCpos.pthre.aligned.e
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Mingbo
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AFNI Message Board
And may I make a suggestion to modify this page:
to emphasize that for different models, the selector actually mean the specific parameters instead of HRF at specific the time points? Initially I thought that if I just use -gltsym: "SYM: A -B', then it will test the difference of time courses of the two HRFs. It was after I saw almost nothing activated that I came to this question.
by
Mingbo
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AFNI Message Board
Hello,
I have a question:
Say, I use SPMG2 to model HRF. And I want to contrast two conditions, say condition A and condition B. In my understanding the first beta value of SPMG2 corresponds to the normal two-gamma function, the second corresponds to its derivative.
So in some sense, the first beta characterize the amplitude of response, the second characterize the delay of the response.
In
by
Mingbo
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AFNI Message Board
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Pages: 123